Exploring the pH-dependent substrate transport mechanism of FocA using molecular dynamics simulation. (Q37440194)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

title

Exploring the pH-dependent substrate transport mechanism of FocA using molecular dynamics simulation (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

author name string

Xiaoying Lv

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Huihui Liu

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Haipeng Gong

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

language of work or name

English

0 references

publication date

1 December 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

number of pages

10

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

volume

105

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

issue

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

page(s)

2714-2723

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

3 March 2020

molecular dynamics simulation

1 reference

based on heuristic

inferred from title

cites work

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

The formate/nitrite transporter family of anion channels

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Coordination of FocA and pyruvate formate-lyase synthesis in Escherichia coli demonstrates preferential translocation of formate over other mixed-acid fermentation products

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Structural and functional characterization of the nitrite channel NirC from Salmonella typhimurium

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

The formate channel FocA exports the products of mixed-acid fermentation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Cytoplasmic domain filter function in the mechanosensitive channel of small conductance

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

pH-dependent gating in a FocA formate channel

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Structure and mechanism of a pentameric formate channel

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Using VMD: an introductory tutorial

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Comparative protein structure modeling using MODELLER

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Scalable molecular dynamics with NAMD

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

H++: a server for estimating pKas and adding missing hydrogens to macromolecules

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

The molecular biology of formate metabolism in enterobacteria.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Molecular basis of proton motive force generation: structure of formate dehydrogenase-N

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Phylogenetic characterization of novel transport protein families revealed by genome analyses

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

HOLE: a program for the analysis of the pore dimensions of ion channel structural models

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Molecular dynamics study of unbinding of the avidin-biotin complex

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

VMD: visual molecular dynamics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

The pore dimensions of gramicidin A.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Expression and operon structure of the sel genes of Escherichia coli and identification of a third selenium-containing formate dehydrogenase isoenzyme.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Pyruvate formate-lyase is not essential for nitrate respiration by Escherichia coli.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Concerted movement in pH-dependent gating of FocA from molecular dynamics simulations.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Good practices in free-energy calculations

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Adaptive biasing force method for scalar and vector free energy calculations

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

The implementation of a fast and accurate QM/MM potential method in Amber

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared withab initioquantum mechanics calculations

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Formate and its role in hydrogen production in Escherichia coli

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Assessing the efficiency of free energy calculation methods

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3882453

Mechanism of regulation of the formate-hydrogenlyase pathway by oxygen, nitrate, and pH: definition of the formate regulon

2 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24359743

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2013.11.006

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

PubMed publication ID

24359743

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24359743%20AND%20SRC:MED&resulttype=core&format=json